Starting phenix.real_space_refine on Sun Jun 15 04:28:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.map" model { file = "/net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o11_49994/06_2025/9o11_49994.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 44 5.16 5 C 5520 2.51 5 N 1356 2.21 5 O 1444 1.98 5 H 8772 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 17136 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "B" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "C" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Chain: "D" Number of atoms: 4284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 4284 Classifications: {'peptide': 261} Link IDs: {'PTRANS': 10, 'TRANS': 250} Time building chain proxies: 8.50, per 1000 atoms: 0.50 Number of scatterers: 17136 At special positions: 0 Unit cell: (119.623, 119.623, 78.015, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 44 16.00 O 1444 8.00 N 1356 7.00 C 5520 6.00 H 8772 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.31 Conformation dependent library (CDL) restraints added in 1.4 seconds 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1992 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 4 sheets defined 83.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 168 through 181 Processing helix chain 'A' and resid 185 through 209 Processing helix chain 'A' and resid 226 through 251 Processing helix chain 'A' and resid 253 through 259 Processing helix chain 'A' and resid 260 through 269 Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.895A pdb=" N TYR A 274 " --> pdb=" O ILE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 302 removed outlier: 4.164A pdb=" N ARG A 294 " --> pdb=" O GLN A 290 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLN A 297 " --> pdb=" O ARG A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 313 removed outlier: 3.627A pdb=" N LEU A 310 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 3.594A pdb=" N GLN A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 354 removed outlier: 3.611A pdb=" N ILE A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 351 " --> pdb=" O SER A 347 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 367 through 376 Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.553A pdb=" N CYS A 398 " --> pdb=" O GLY A 394 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 426 removed outlier: 3.853A pdb=" N GLN A 423 " --> pdb=" O PHE A 419 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS A 424 " --> pdb=" O TYR A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 209 Processing helix chain 'B' and resid 226 through 251 Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.912A pdb=" N GLY B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 261 through 269 removed outlier: 3.774A pdb=" N ASP B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU B 267 " --> pdb=" O ASN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 281 removed outlier: 3.897A pdb=" N TYR B 274 " --> pdb=" O ILE B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 302 removed outlier: 4.753A pdb=" N ARG B 294 " --> pdb=" O GLN B 290 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLN B 297 " --> pdb=" O ARG B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.630A pdb=" N LEU B 310 " --> pdb=" O ILE B 307 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG B 312 " --> pdb=" O LYS B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 327 removed outlier: 3.660A pdb=" N GLN B 318 " --> pdb=" O SER B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 354 removed outlier: 3.697A pdb=" N ILE B 335 " --> pdb=" O LEU B 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 351 " --> pdb=" O SER B 347 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA B 352 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 366 No H-bonds generated for 'chain 'B' and resid 364 through 366' Processing helix chain 'B' and resid 367 through 376 removed outlier: 3.516A pdb=" N THR B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 406 removed outlier: 3.728A pdb=" N CYS B 398 " --> pdb=" O GLY B 394 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ILE B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 426 removed outlier: 3.730A pdb=" N GLN B 423 " --> pdb=" O PHE B 419 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LYS B 424 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 181 Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 209 Processing helix chain 'C' and resid 226 through 251 Processing helix chain 'C' and resid 253 through 260 removed outlier: 3.891A pdb=" N GLY C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.788A pdb=" N LEU C 267 " --> pdb=" O ASN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.792A pdb=" N TYR C 274 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE C 277 " --> pdb=" O TYR C 273 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 302 Processing helix chain 'C' and resid 303 through 313 removed outlier: 3.627A pdb=" N LEU C 310 " --> pdb=" O ILE C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 327 removed outlier: 3.590A pdb=" N GLN C 318 " --> pdb=" O SER C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 327 through 354 removed outlier: 3.680A pdb=" N ILE C 335 " --> pdb=" O LEU C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 366 No H-bonds generated for 'chain 'C' and resid 364 through 366' Processing helix chain 'C' and resid 367 through 376 removed outlier: 3.509A pdb=" N THR C 376 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.781A pdb=" N ILE C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL C 402 " --> pdb=" O CYS C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 426 removed outlier: 3.699A pdb=" N GLN C 423 " --> pdb=" O PHE C 419 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS C 424 " --> pdb=" O TYR C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 181 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 185 through 209 Processing helix chain 'D' and resid 226 through 251 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.930A pdb=" N GLY D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 269 removed outlier: 3.785A pdb=" N LEU D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 282 removed outlier: 3.726A pdb=" N TYR D 274 " --> pdb=" O ILE D 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 302 Processing helix chain 'D' and resid 303 through 313 removed outlier: 3.669A pdb=" N LEU D 310 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 327 removed outlier: 3.579A pdb=" N GLN D 318 " --> pdb=" O SER D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 354 removed outlier: 3.785A pdb=" N ILE D 335 " --> pdb=" O LEU D 331 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE D 351 " --> pdb=" O SER D 347 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 352 " --> pdb=" O LEU D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 367 through 376 removed outlier: 3.513A pdb=" N THR D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.561A pdb=" N CYS D 398 " --> pdb=" O GLY D 394 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE D 399 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL D 402 " --> pdb=" O CYS D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 426 removed outlier: 3.966A pdb=" N GLN D 423 " --> pdb=" O PHE D 419 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AA2, first strand: chain 'B' and resid 216 through 217 Processing sheet with id=AA3, first strand: chain 'C' and resid 216 through 217 Processing sheet with id=AA4, first strand: chain 'D' and resid 216 through 217 596 hydrogen bonds defined for protein. 1695 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.74 Time building geometry restraints manager: 5.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8752 1.03 - 1.23: 29 1.23 - 1.42: 3443 1.42 - 1.62: 5028 1.62 - 1.81: 68 Bond restraints: 17320 Sorted by residual: bond pdb=" N CYS D 167 " pdb=" CA CYS D 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.10e+00 bond pdb=" N CYS B 167 " pdb=" CA CYS B 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS A 167 " pdb=" CA CYS A 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N CYS C 167 " pdb=" CA CYS C 167 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.95e+00 bond pdb=" N CYS A 167 " pdb=" H CYS A 167 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.33e+00 ... (remaining 17315 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 28231 0.92 - 1.84: 3045 1.84 - 2.76: 157 2.76 - 3.68: 36 3.68 - 4.60: 23 Bond angle restraints: 31492 Sorted by residual: angle pdb=" N LYS C 424 " pdb=" CA LYS C 424 " pdb=" C LYS C 424 " ideal model delta sigma weight residual 114.56 110.22 4.34 1.27e+00 6.20e-01 1.17e+01 angle pdb=" CA LYS C 424 " pdb=" C LYS C 424 " pdb=" N ARG C 425 " ideal model delta sigma weight residual 119.26 117.15 2.11 1.14e+00 7.69e-01 3.44e+00 angle pdb=" CA TYR A 380 " pdb=" CB TYR A 380 " pdb=" CG TYR A 380 " ideal model delta sigma weight residual 113.90 117.19 -3.29 1.80e+00 3.09e-01 3.35e+00 angle pdb=" CA TYR B 380 " pdb=" CB TYR B 380 " pdb=" CG TYR B 380 " ideal model delta sigma weight residual 113.90 117.12 -3.22 1.80e+00 3.09e-01 3.20e+00 angle pdb=" CA TYR C 380 " pdb=" CB TYR C 380 " pdb=" CG TYR C 380 " ideal model delta sigma weight residual 113.90 117.10 -3.20 1.80e+00 3.09e-01 3.16e+00 ... (remaining 31487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7404 17.98 - 35.96: 451 35.96 - 53.94: 165 53.94 - 71.92: 24 71.92 - 89.90: 16 Dihedral angle restraints: 8060 sinusoidal: 4384 harmonic: 3676 Sorted by residual: dihedral pdb=" CA ARG B 425 " pdb=" C ARG B 425 " pdb=" N GLN B 426 " pdb=" CA GLN B 426 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA ARG A 425 " pdb=" C ARG A 425 " pdb=" N GLN A 426 " pdb=" CA GLN A 426 " ideal model delta harmonic sigma weight residual -180.00 -160.81 -19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TYR D 380 " pdb=" C TYR D 380 " pdb=" N GLY D 381 " pdb=" CA GLY D 381 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 8057 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 729 0.023 - 0.047: 387 0.047 - 0.070: 151 0.070 - 0.094: 68 0.094 - 0.117: 29 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CA PRO D 410 " pdb=" N PRO D 410 " pdb=" C PRO D 410 " pdb=" CB PRO D 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.43e-01 chirality pdb=" CA PRO B 410 " pdb=" N PRO B 410 " pdb=" C PRO B 410 " pdb=" CB PRO B 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.40e-01 chirality pdb=" CA PRO C 410 " pdb=" N PRO C 410 " pdb=" C PRO C 410 " pdb=" CB PRO C 410 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.33e-01 ... (remaining 1361 not shown) Planarity restraints: 2408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU D 418 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.87e+00 pdb=" C GLU D 418 " 0.029 2.00e-02 2.50e+03 pdb=" O GLU D 418 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE D 419 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 407 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO A 408 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 408 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 408 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 407 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO D 408 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO D 408 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 408 " 0.022 5.00e-02 4.00e+02 ... (remaining 2405 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1149 2.22 - 2.81: 36058 2.81 - 3.41: 44318 3.41 - 4.00: 55644 4.00 - 4.60: 86570 Nonbonded interactions: 223739 Sorted by model distance: nonbonded pdb=" OD2 ASP A 266 " pdb="HH21 ARG A 312 " model vdw 1.622 2.450 nonbonded pdb=" OE2 GLU B 353 " pdb=" HG1 THR B 387 " model vdw 1.627 2.450 nonbonded pdb=" OG SER D 327 " pdb="HD21 ASN D 415 " model vdw 1.649 2.450 nonbonded pdb=" OG SER B 327 " pdb="HD21 ASN B 415 " model vdw 1.655 2.450 nonbonded pdb=" OG SER C 327 " pdb="HD21 ASN C 415 " model vdw 1.663 2.450 ... (remaining 223734 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.260 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.540 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8548 Z= 0.153 Angle : 0.489 4.448 11572 Z= 0.268 Chirality : 0.037 0.117 1364 Planarity : 0.004 0.039 1408 Dihedral : 13.208 89.904 3140 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.11 % Allowed : 7.76 % Favored : 92.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.27), residues: 1036 helix: 1.80 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 370 HIS 0.002 0.001 HIS D 231 PHE 0.007 0.001 PHE C 416 TYR 0.015 0.002 TYR A 273 ARG 0.004 0.001 ARG B 303 Details of bonding type rmsd hydrogen bonds : bond 0.11243 ( 596) hydrogen bonds : angle 4.14936 ( 1695) covalent geometry : bond 0.00364 ( 8548) covalent geometry : angle 0.48877 (11572) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.8755 (m-30) cc_final: 0.8479 (m-30) REVERT: A 226 ASN cc_start: 0.8665 (t0) cc_final: 0.8427 (t0) REVERT: B 177 ASP cc_start: 0.8742 (m-30) cc_final: 0.8538 (m-30) REVERT: B 180 GLU cc_start: 0.8603 (tt0) cc_final: 0.8216 (tt0) REVERT: B 226 ASN cc_start: 0.8676 (t0) cc_final: 0.8332 (t0) REVERT: B 297 GLN cc_start: 0.9113 (mm110) cc_final: 0.8876 (mm-40) REVERT: C 177 ASP cc_start: 0.8576 (m-30) cc_final: 0.8369 (m-30) REVERT: C 180 GLU cc_start: 0.8528 (tt0) cc_final: 0.8205 (tt0) REVERT: C 226 ASN cc_start: 0.8683 (t0) cc_final: 0.8398 (t0) REVERT: C 297 GLN cc_start: 0.9020 (mm110) cc_final: 0.8776 (mm110) REVERT: D 177 ASP cc_start: 0.8693 (m-30) cc_final: 0.8410 (m-30) REVERT: D 180 GLU cc_start: 0.8541 (tt0) cc_final: 0.8193 (tt0) REVERT: D 226 ASN cc_start: 0.8673 (t0) cc_final: 0.8395 (t0) outliers start: 1 outliers final: 1 residues processed: 248 average time/residue: 0.5622 time to fit residues: 179.2324 Evaluate side-chains 198 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 331 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 GLN B 423 GLN C 263 ASN C 291 ASN C 423 GLN D 209 ASN D 291 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086254 restraints weight = 46202.803| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.28 r_work: 0.3124 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8548 Z= 0.166 Angle : 0.565 6.779 11572 Z= 0.304 Chirality : 0.036 0.111 1364 Planarity : 0.005 0.049 1408 Dihedral : 4.003 44.291 1114 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.75 % Allowed : 11.64 % Favored : 87.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.27), residues: 1036 helix: 1.93 (0.19), residues: 808 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 370 HIS 0.002 0.001 HIS B 231 PHE 0.011 0.001 PHE C 416 TYR 0.012 0.001 TYR D 380 ARG 0.004 0.000 ARG D 247 Details of bonding type rmsd hydrogen bonds : bond 0.04522 ( 596) hydrogen bonds : angle 3.77552 ( 1695) covalent geometry : bond 0.00373 ( 8548) covalent geometry : angle 0.56484 (11572) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 209 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9123 (m-30) cc_final: 0.8765 (m-30) REVERT: A 180 GLU cc_start: 0.9158 (tt0) cc_final: 0.8806 (mt-10) REVERT: A 226 ASN cc_start: 0.8315 (t0) cc_final: 0.7840 (t0) REVERT: A 243 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8351 (mt-10) REVERT: B 177 ASP cc_start: 0.8988 (m-30) cc_final: 0.8726 (m-30) REVERT: B 180 GLU cc_start: 0.9012 (tt0) cc_final: 0.8735 (tt0) REVERT: B 226 ASN cc_start: 0.8272 (t0) cc_final: 0.7585 (t0) REVERT: B 228 GLN cc_start: 0.8740 (mp10) cc_final: 0.8324 (mp10) REVERT: C 177 ASP cc_start: 0.8920 (m-30) cc_final: 0.8704 (m-30) REVERT: C 180 GLU cc_start: 0.8954 (tt0) cc_final: 0.8747 (tt0) REVERT: C 226 ASN cc_start: 0.8287 (t0) cc_final: 0.7844 (t0) REVERT: C 243 GLU cc_start: 0.8726 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 297 GLN cc_start: 0.9130 (mm110) cc_final: 0.8828 (mm110) REVERT: D 177 ASP cc_start: 0.9013 (m-30) cc_final: 0.8703 (m-30) REVERT: D 180 GLU cc_start: 0.9000 (tt0) cc_final: 0.8749 (tt0) outliers start: 7 outliers final: 5 residues processed: 212 average time/residue: 0.4895 time to fit residues: 137.7700 Evaluate side-chains 207 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 202 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain D residue 266 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 71 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 76 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 66 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.124665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086380 restraints weight = 45777.980| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.28 r_work: 0.3164 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8548 Z= 0.132 Angle : 0.525 7.837 11572 Z= 0.276 Chirality : 0.035 0.111 1364 Planarity : 0.004 0.035 1408 Dihedral : 3.615 24.002 1112 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.08 % Allowed : 11.42 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.28), residues: 1036 helix: 2.17 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -1.26 (0.37), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 370 HIS 0.002 0.001 HIS B 231 PHE 0.019 0.001 PHE A 289 TYR 0.011 0.001 TYR A 380 ARG 0.004 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 596) hydrogen bonds : angle 3.64325 ( 1695) covalent geometry : bond 0.00302 ( 8548) covalent geometry : angle 0.52488 (11572) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 204 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9583 (mmtp) cc_final: 0.9366 (mtpt) REVERT: A 177 ASP cc_start: 0.9101 (m-30) cc_final: 0.8740 (m-30) REVERT: A 226 ASN cc_start: 0.8277 (t0) cc_final: 0.7838 (t0) REVERT: A 294 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8173 (ptp-170) REVERT: A 426 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 177 ASP cc_start: 0.8950 (m-30) cc_final: 0.8698 (m-30) REVERT: B 180 GLU cc_start: 0.8994 (tt0) cc_final: 0.8714 (tt0) REVERT: B 226 ASN cc_start: 0.8206 (t0) cc_final: 0.7544 (t0) REVERT: B 228 GLN cc_start: 0.8727 (mp10) cc_final: 0.8372 (mp10) REVERT: B 243 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8225 (mt-10) REVERT: C 177 ASP cc_start: 0.8882 (m-30) cc_final: 0.8677 (m-30) REVERT: C 243 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8507 (mt-10) REVERT: C 297 GLN cc_start: 0.9103 (mm110) cc_final: 0.8805 (mm110) REVERT: D 177 ASP cc_start: 0.8982 (m-30) cc_final: 0.8675 (m-30) REVERT: D 180 GLU cc_start: 0.9008 (tt0) cc_final: 0.8781 (tt0) REVERT: D 243 GLU cc_start: 0.8762 (tt0) cc_final: 0.8505 (mt-10) outliers start: 10 outliers final: 6 residues processed: 206 average time/residue: 0.4719 time to fit residues: 130.3772 Evaluate side-chains 202 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 196 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 94 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.125033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086426 restraints weight = 45489.151| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 3.31 r_work: 0.3136 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8548 Z= 0.118 Angle : 0.510 7.168 11572 Z= 0.267 Chirality : 0.035 0.112 1364 Planarity : 0.004 0.037 1408 Dihedral : 3.486 22.233 1112 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.19 % Allowed : 12.50 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.28), residues: 1036 helix: 2.32 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -1.15 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 370 HIS 0.002 0.001 HIS B 231 PHE 0.009 0.001 PHE A 289 TYR 0.011 0.001 TYR B 380 ARG 0.004 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 596) hydrogen bonds : angle 3.56485 ( 1695) covalent geometry : bond 0.00272 ( 8548) covalent geometry : angle 0.51009 (11572) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9572 (mmtp) cc_final: 0.9367 (mtpt) REVERT: A 177 ASP cc_start: 0.9091 (m-30) cc_final: 0.8731 (m-30) REVERT: A 226 ASN cc_start: 0.8292 (t0) cc_final: 0.7881 (t0) REVERT: A 243 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8339 (mt-10) REVERT: A 294 ARG cc_start: 0.8660 (ttm110) cc_final: 0.8229 (ptp-170) REVERT: A 426 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 177 ASP cc_start: 0.8967 (m-30) cc_final: 0.8722 (m-30) REVERT: B 180 GLU cc_start: 0.9042 (tt0) cc_final: 0.8762 (tt0) REVERT: B 226 ASN cc_start: 0.8266 (t0) cc_final: 0.7513 (t0) REVERT: B 228 GLN cc_start: 0.8754 (mp10) cc_final: 0.8335 (mp10) REVERT: B 243 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8410 (mt-10) REVERT: C 177 ASP cc_start: 0.8874 (m-30) cc_final: 0.8662 (m-30) REVERT: C 228 GLN cc_start: 0.8776 (mp10) cc_final: 0.8396 (mp10) REVERT: C 243 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8408 (mt-10) REVERT: C 297 GLN cc_start: 0.9122 (mm110) cc_final: 0.8776 (mm110) REVERT: D 177 ASP cc_start: 0.8998 (m-30) cc_final: 0.8685 (m-30) REVERT: D 180 GLU cc_start: 0.9019 (tt0) cc_final: 0.8772 (tt0) REVERT: D 243 GLU cc_start: 0.8826 (tt0) cc_final: 0.8549 (mt-10) outliers start: 11 outliers final: 9 residues processed: 204 average time/residue: 0.5344 time to fit residues: 151.0647 Evaluate side-chains 204 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 195 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 355 ASP Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 11 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 83 optimal weight: 0.0070 chunk 64 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 overall best weight: 2.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.124471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.085877 restraints weight = 46189.946| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 3.30 r_work: 0.3085 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8548 Z= 0.134 Angle : 0.521 6.883 11572 Z= 0.273 Chirality : 0.035 0.112 1364 Planarity : 0.004 0.040 1408 Dihedral : 3.406 20.418 1112 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.40 % Allowed : 13.47 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.28), residues: 1036 helix: 2.37 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -1.11 (0.38), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 370 HIS 0.002 0.001 HIS D 231 PHE 0.010 0.001 PHE C 257 TYR 0.012 0.001 TYR B 380 ARG 0.004 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 596) hydrogen bonds : angle 3.59770 ( 1695) covalent geometry : bond 0.00311 ( 8548) covalent geometry : angle 0.52076 (11572) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 203 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9573 (mmtp) cc_final: 0.9371 (mtpt) REVERT: A 177 ASP cc_start: 0.9067 (m-30) cc_final: 0.8705 (m-30) REVERT: A 226 ASN cc_start: 0.8314 (t0) cc_final: 0.7917 (t0) REVERT: A 243 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 294 ARG cc_start: 0.8687 (ttm110) cc_final: 0.8246 (ptp-170) REVERT: A 426 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 177 ASP cc_start: 0.8988 (m-30) cc_final: 0.8743 (m-30) REVERT: B 180 GLU cc_start: 0.9008 (tt0) cc_final: 0.8717 (tt0) REVERT: B 226 ASN cc_start: 0.8315 (t0) cc_final: 0.7565 (t0) REVERT: B 228 GLN cc_start: 0.8793 (mp10) cc_final: 0.8409 (mp10) REVERT: B 243 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 177 ASP cc_start: 0.8869 (m-30) cc_final: 0.8650 (m-30) REVERT: C 226 ASN cc_start: 0.8225 (t0) cc_final: 0.7553 (t0) REVERT: C 228 GLN cc_start: 0.8791 (mp10) cc_final: 0.8430 (mp10) REVERT: C 243 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8394 (mt-10) REVERT: D 177 ASP cc_start: 0.8991 (m-30) cc_final: 0.8679 (m-30) REVERT: D 180 GLU cc_start: 0.9017 (tt0) cc_final: 0.8757 (tt0) REVERT: D 226 ASN cc_start: 0.8234 (t0) cc_final: 0.7647 (t0) REVERT: D 288 GLN cc_start: 0.7379 (pm20) cc_final: 0.7178 (pm20) outliers start: 13 outliers final: 10 residues processed: 206 average time/residue: 0.5390 time to fit residues: 152.5560 Evaluate side-chains 208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 61 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 74 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081479 restraints weight = 45647.411| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.28 r_work: 0.2922 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8548 Z= 0.109 Angle : 0.511 7.388 11572 Z= 0.265 Chirality : 0.034 0.111 1364 Planarity : 0.004 0.033 1408 Dihedral : 3.312 18.621 1112 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.40 % Allowed : 14.33 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.70 (0.28), residues: 1036 helix: 2.50 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.93 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 370 HIS 0.002 0.001 HIS D 231 PHE 0.009 0.001 PHE A 289 TYR 0.011 0.001 TYR B 380 ARG 0.004 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 596) hydrogen bonds : angle 3.46697 ( 1695) covalent geometry : bond 0.00250 ( 8548) covalent geometry : angle 0.51056 (11572) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 205 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 174 LYS cc_start: 0.9590 (mmtp) cc_final: 0.9378 (mtpt) REVERT: A 177 ASP cc_start: 0.9071 (m-30) cc_final: 0.8740 (m-30) REVERT: A 226 ASN cc_start: 0.8286 (t0) cc_final: 0.7896 (t0) REVERT: A 243 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8316 (mt-10) REVERT: A 294 ARG cc_start: 0.8730 (ttm110) cc_final: 0.8380 (ptp-170) REVERT: A 426 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8440 (tm-30) REVERT: B 177 ASP cc_start: 0.8975 (m-30) cc_final: 0.8738 (m-30) REVERT: B 180 GLU cc_start: 0.8992 (tt0) cc_final: 0.8697 (tt0) REVERT: B 226 ASN cc_start: 0.8295 (t0) cc_final: 0.7511 (t0) REVERT: B 228 GLN cc_start: 0.8753 (mp10) cc_final: 0.8361 (mp10) REVERT: B 243 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8259 (mt-10) REVERT: C 177 ASP cc_start: 0.8872 (m-30) cc_final: 0.8664 (m-30) REVERT: C 226 ASN cc_start: 0.8225 (t0) cc_final: 0.7506 (t0) REVERT: C 228 GLN cc_start: 0.8767 (mp10) cc_final: 0.8421 (mp10) REVERT: C 243 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8422 (mt-10) REVERT: D 177 ASP cc_start: 0.8959 (m-30) cc_final: 0.8642 (m-30) REVERT: D 180 GLU cc_start: 0.9011 (tt0) cc_final: 0.8756 (tt0) REVERT: D 228 GLN cc_start: 0.8792 (mp10) cc_final: 0.8503 (mp10) REVERT: D 243 GLU cc_start: 0.8928 (tt0) cc_final: 0.8704 (mt-10) outliers start: 13 outliers final: 11 residues processed: 207 average time/residue: 0.4458 time to fit residues: 125.8154 Evaluate side-chains 210 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 199 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 340 MET Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.120148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.080557 restraints weight = 45491.875| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.27 r_work: 0.2913 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8548 Z= 0.143 Angle : 0.522 7.602 11572 Z= 0.273 Chirality : 0.035 0.114 1364 Planarity : 0.004 0.030 1408 Dihedral : 3.292 17.611 1112 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.08 % Allowed : 15.19 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.28), residues: 1036 helix: 2.48 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.98 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 370 HIS 0.001 0.000 HIS D 231 PHE 0.009 0.001 PHE C 257 TYR 0.011 0.001 TYR B 380 ARG 0.003 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 596) hydrogen bonds : angle 3.56237 ( 1695) covalent geometry : bond 0.00331 ( 8548) covalent geometry : angle 0.52193 (11572) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9079 (m-30) cc_final: 0.8740 (m-30) REVERT: A 226 ASN cc_start: 0.8316 (t0) cc_final: 0.7933 (t0) REVERT: A 243 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8481 (mt-10) REVERT: A 294 ARG cc_start: 0.8735 (ttm110) cc_final: 0.8362 (ptp-170) REVERT: A 426 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8435 (tm-30) REVERT: B 177 ASP cc_start: 0.8986 (m-30) cc_final: 0.8747 (m-30) REVERT: B 180 GLU cc_start: 0.8960 (tt0) cc_final: 0.8640 (tt0) REVERT: B 226 ASN cc_start: 0.8347 (t0) cc_final: 0.7598 (t0) REVERT: B 228 GLN cc_start: 0.8825 (mp10) cc_final: 0.8451 (mp10) REVERT: B 243 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8268 (mt-10) REVERT: C 177 ASP cc_start: 0.8886 (m-30) cc_final: 0.8677 (m-30) REVERT: C 226 ASN cc_start: 0.8295 (t0) cc_final: 0.7928 (t0) REVERT: C 228 GLN cc_start: 0.8800 (mp10) cc_final: 0.8363 (mp10) REVERT: C 243 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8386 (mt-10) REVERT: C 297 GLN cc_start: 0.9137 (mm110) cc_final: 0.8809 (mm110) REVERT: D 177 ASP cc_start: 0.8940 (m-30) cc_final: 0.8615 (m-30) REVERT: D 180 GLU cc_start: 0.8964 (tt0) cc_final: 0.8677 (tt0) REVERT: D 228 GLN cc_start: 0.8809 (mp10) cc_final: 0.8450 (mp10) REVERT: D 243 GLU cc_start: 0.8934 (tt0) cc_final: 0.8710 (mt-10) REVERT: D 288 GLN cc_start: 0.7276 (pm20) cc_final: 0.7061 (pm20) outliers start: 10 outliers final: 10 residues processed: 203 average time/residue: 0.5369 time to fit residues: 149.2890 Evaluate side-chains 208 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 198 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.4980 chunk 16 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.120665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081512 restraints weight = 45791.668| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 3.22 r_work: 0.2904 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8548 Z= 0.162 Angle : 0.541 6.804 11572 Z= 0.285 Chirality : 0.036 0.114 1364 Planarity : 0.004 0.057 1408 Dihedral : 3.328 19.149 1112 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.72 % Allowed : 14.87 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.28), residues: 1036 helix: 2.47 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 239 HIS 0.001 0.001 HIS D 231 PHE 0.009 0.001 PHE C 257 TYR 0.012 0.001 TYR A 380 ARG 0.007 0.000 ARG D 293 Details of bonding type rmsd hydrogen bonds : bond 0.03913 ( 596) hydrogen bonds : angle 3.63871 ( 1695) covalent geometry : bond 0.00375 ( 8548) covalent geometry : angle 0.54149 (11572) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9084 (m-30) cc_final: 0.8714 (m-30) REVERT: A 226 ASN cc_start: 0.8357 (t0) cc_final: 0.7960 (t0) REVERT: A 243 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8482 (mt-10) REVERT: A 294 ARG cc_start: 0.8751 (ttm110) cc_final: 0.8414 (ptp-170) REVERT: A 426 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8457 (tm-30) REVERT: B 177 ASP cc_start: 0.8995 (m-30) cc_final: 0.8757 (m-30) REVERT: B 180 GLU cc_start: 0.8961 (tt0) cc_final: 0.8663 (tt0) REVERT: B 226 ASN cc_start: 0.8346 (t0) cc_final: 0.7583 (t0) REVERT: B 228 GLN cc_start: 0.8847 (mp10) cc_final: 0.8485 (mp10) REVERT: B 243 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8285 (mt-10) REVERT: B 353 GLU cc_start: 0.8825 (mm-30) cc_final: 0.8338 (mm-30) REVERT: C 177 ASP cc_start: 0.8893 (m-30) cc_final: 0.8686 (m-30) REVERT: C 226 ASN cc_start: 0.8321 (t0) cc_final: 0.7966 (t0) REVERT: C 228 GLN cc_start: 0.8810 (mp10) cc_final: 0.8379 (mp10) REVERT: C 243 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8395 (mt-10) REVERT: C 297 GLN cc_start: 0.9142 (mm110) cc_final: 0.8813 (mm110) REVERT: D 177 ASP cc_start: 0.8960 (m-30) cc_final: 0.8634 (m-30) REVERT: D 180 GLU cc_start: 0.8981 (tt0) cc_final: 0.8713 (tt0) REVERT: D 226 ASN cc_start: 0.8228 (t0) cc_final: 0.7551 (t0) REVERT: D 228 GLN cc_start: 0.8834 (mp10) cc_final: 0.8477 (mp10) REVERT: D 243 GLU cc_start: 0.8952 (tt0) cc_final: 0.8635 (mt-10) REVERT: D 288 GLN cc_start: 0.7310 (pm20) cc_final: 0.7093 (pm20) outliers start: 16 outliers final: 13 residues processed: 207 average time/residue: 0.4571 time to fit residues: 129.1484 Evaluate side-chains 214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 266 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 301 ILE Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 229 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.120745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.081643 restraints weight = 45820.195| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.25 r_work: 0.2896 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8548 Z= 0.145 Angle : 0.539 6.837 11572 Z= 0.282 Chirality : 0.035 0.114 1364 Planarity : 0.004 0.027 1408 Dihedral : 3.308 18.367 1112 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.19 % Allowed : 15.84 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.28), residues: 1036 helix: 2.50 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.87 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 370 HIS 0.001 0.001 HIS B 231 PHE 0.009 0.001 PHE C 257 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 596) hydrogen bonds : angle 3.57605 ( 1695) covalent geometry : bond 0.00337 ( 8548) covalent geometry : angle 0.53855 (11572) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 204 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9064 (m-30) cc_final: 0.8681 (m-30) REVERT: A 226 ASN cc_start: 0.8368 (t0) cc_final: 0.7976 (t0) REVERT: A 243 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 294 ARG cc_start: 0.8765 (ttm110) cc_final: 0.8445 (ptp-170) REVERT: A 426 GLN cc_start: 0.8787 (tm-30) cc_final: 0.8488 (tm-30) REVERT: B 177 ASP cc_start: 0.8985 (m-30) cc_final: 0.8745 (m-30) REVERT: B 180 GLU cc_start: 0.8962 (tt0) cc_final: 0.8664 (tt0) REVERT: B 226 ASN cc_start: 0.8357 (t0) cc_final: 0.7593 (t0) REVERT: B 228 GLN cc_start: 0.8871 (mp10) cc_final: 0.8518 (mp10) REVERT: B 243 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8303 (mt-10) REVERT: B 353 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8328 (mm-30) REVERT: C 177 ASP cc_start: 0.8899 (m-30) cc_final: 0.8679 (m-30) REVERT: C 226 ASN cc_start: 0.8354 (t0) cc_final: 0.7960 (t0) REVERT: C 228 GLN cc_start: 0.8822 (mp10) cc_final: 0.8361 (mp10) REVERT: C 297 GLN cc_start: 0.9148 (mm110) cc_final: 0.8809 (mm110) REVERT: D 177 ASP cc_start: 0.8997 (m-30) cc_final: 0.8677 (m-30) REVERT: D 180 GLU cc_start: 0.8984 (tt0) cc_final: 0.8712 (tt0) REVERT: D 226 ASN cc_start: 0.8253 (t0) cc_final: 0.7538 (t0) REVERT: D 228 GLN cc_start: 0.8851 (mp10) cc_final: 0.8466 (mp10) REVERT: D 243 GLU cc_start: 0.8955 (tt0) cc_final: 0.8694 (mt-10) REVERT: D 288 GLN cc_start: 0.7376 (pm20) cc_final: 0.7151 (pm20) outliers start: 11 outliers final: 10 residues processed: 207 average time/residue: 0.4788 time to fit residues: 133.5706 Evaluate side-chains 210 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 GLN B 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.121800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.082614 restraints weight = 45279.629| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.24 r_work: 0.2911 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8548 Z= 0.111 Angle : 0.522 6.712 11572 Z= 0.270 Chirality : 0.035 0.113 1364 Planarity : 0.004 0.045 1408 Dihedral : 3.250 17.307 1112 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.19 % Allowed : 16.59 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.28), residues: 1036 helix: 2.64 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.74 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 370 HIS 0.001 0.000 HIS C 231 PHE 0.009 0.001 PHE C 198 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG D 312 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 596) hydrogen bonds : angle 3.44639 ( 1695) covalent geometry : bond 0.00260 ( 8548) covalent geometry : angle 0.52242 (11572) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2072 Ramachandran restraints generated. 1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 203 time to evaluate : 1.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ASP cc_start: 0.9054 (m-30) cc_final: 0.8701 (m-30) REVERT: A 226 ASN cc_start: 0.8330 (t0) cc_final: 0.7950 (t0) REVERT: A 243 GLU cc_start: 0.8741 (mt-10) cc_final: 0.8483 (mt-10) REVERT: A 426 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8505 (tm-30) REVERT: B 177 ASP cc_start: 0.8968 (m-30) cc_final: 0.8727 (m-30) REVERT: B 180 GLU cc_start: 0.8966 (tt0) cc_final: 0.8606 (tt0) REVERT: B 226 ASN cc_start: 0.8311 (t0) cc_final: 0.7543 (t0) REVERT: B 228 GLN cc_start: 0.8847 (mp10) cc_final: 0.8490 (mp10) REVERT: B 243 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 353 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8245 (mm-30) REVERT: C 177 ASP cc_start: 0.8879 (m-30) cc_final: 0.8679 (m-30) REVERT: C 180 GLU cc_start: 0.9095 (tt0) cc_final: 0.8760 (mt-10) REVERT: C 226 ASN cc_start: 0.8310 (t0) cc_final: 0.7889 (t0) REVERT: C 228 GLN cc_start: 0.8813 (mp10) cc_final: 0.8335 (mp10) REVERT: C 243 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8311 (mt-10) REVERT: C 297 GLN cc_start: 0.9139 (mm110) cc_final: 0.8791 (mm110) REVERT: C 423 GLN cc_start: 0.7787 (pt0) cc_final: 0.7503 (pp30) REVERT: D 177 ASP cc_start: 0.8978 (m-30) cc_final: 0.8656 (m-30) REVERT: D 180 GLU cc_start: 0.8983 (tt0) cc_final: 0.8715 (tt0) REVERT: D 228 GLN cc_start: 0.8841 (mp10) cc_final: 0.8458 (mp10) REVERT: D 243 GLU cc_start: 0.8956 (tt0) cc_final: 0.8675 (mt-10) outliers start: 11 outliers final: 10 residues processed: 206 average time/residue: 0.4502 time to fit residues: 126.9364 Evaluate side-chains 212 residues out of total 928 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 266 ASP Chi-restraints excluded: chain D residue 380 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 48 optimal weight: 0.0060 chunk 58 optimal weight: 0.0970 chunk 50 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 52 optimal weight: 6.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.123634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.084535 restraints weight = 44778.614| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.20 r_work: 0.2958 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 8548 Z= 0.101 Angle : 0.520 6.695 11572 Z= 0.266 Chirality : 0.034 0.111 1364 Planarity : 0.004 0.041 1408 Dihedral : 3.164 16.620 1112 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.97 % Allowed : 16.49 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.28), residues: 1036 helix: 2.77 (0.20), residues: 808 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 370 HIS 0.002 0.000 HIS B 231 PHE 0.009 0.001 PHE B 289 TYR 0.012 0.001 TYR C 380 ARG 0.003 0.000 ARG C 300 Details of bonding type rmsd hydrogen bonds : bond 0.03262 ( 596) hydrogen bonds : angle 3.30952 ( 1695) covalent geometry : bond 0.00236 ( 8548) covalent geometry : angle 0.52044 (11572) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8122.90 seconds wall clock time: 141 minutes 47.33 seconds (8507.33 seconds total)